Per-and polyfluoroalkyl substances (PFAS) are a group of synthetic, highly fluorinated, and emerging chemicals that are reported to be used for both industrial and domestic applications. Several PFAS have demonstrated persistent, bioaccumulative and toxic tendencies in marine organisms. Therefore, this research aims to characterize and quantify these compounds in both recreational fisheries and surface water samples, including estimating their bioaccumulation potentials. In addition, we assessed the potential contribution of biomonitoring tools such as oxidative stressors and morphological index on fish and ecological health. Finally, human health risk assessment was performed based on available toxicological data on limited PFAS. All PFAS were detected in at least one sample except for N-EtFOSAA in lobster which was below the method detection limit. ƩPFAS body burden ranged from 0.15 to 3.40 ng/g wet weight (ww) in blackfin tuna samples and 0.37–5.15 ng/g ww in lobster samples, respectively. Wilcoxon rank paired test (α = 0.05) shows that there is statistical significance (ρ < 0.05) of ƩPFAS between species. Bioaccumulation factors (BAF) suggest an increasing trend in PFAS classes (PFCAs < PFSAs < FTSs), with higher BAFs observed in tuna compared to lobster. Long-chain PFESAs and FASAA were reported at higher concentrations in lobster compared to Blackfin tuna due to their bioavailability through sediment-sorption interactions. Although Fulton’s condition factor (FCF) indicates healthy fish conditions, oxidative stress biomarkers suggest that tuna and lobster might be under stress, which can weaken their immune system against exposure to emerging contaminants such as PFAS. Hazard risk (HR) suggests a low risk to human health based on the consumption of the studied species; however, the risk of contaminant exposure may be higher than estimated. This study is aimed at improving food safety by providing better understanding of how PFAS infiltrate into human diet and incorporating data on influence of contaminant exposure and environmental stressors on marine health.